• Molecules and Cells
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• 제39권3호
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• pp.211-216
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• 2016

CYP107W1 from Streptomyces avermitilis is a cytochrome P450 enzyme involved in the biosynthesis of macrolide oligomycin A. A previous study reported that CYP107W1 regioselectively hydroxylated C12 of oligomycin C to produce oligomycin A, and the crystal structure of ligand free CYP107W1 was determined. Here, we analyzed the structural properties of the CYP107W1-oligomycin A complex and characterized the functional role of the Trp178 residue in CYP107W1. The crystal structure of the CYP107W1 complex with oligomycin A was determined at a resolution of $2.6{\AA}$. Oligomycin A is bound in the substrate access channel on the upper side of the prosthetic heme mainly by hydrophobic interactions. In particular, the Trp178 residue in the active site intercalates into the large macrolide ring, thereby guiding the substrate into the correct binding orientation for a productive P450 reaction. A Trp178 to Gly mutation resulted in the distortion of binding titration spectra with oligomycin A, whereas binding spectra with azoles were not affected. The Gly178 mutant's catalytic turnover number for the 12-hydroxylation reaction of oligomycin C was highly reduced. These results indicate that Trp178, located in the open pocket of the active site, may be a critical residue for the productive binding conformation of large macrolide substrates.

• KSII Transactions on Internet and Information Systems (TIIS)
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• 제17권8호
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• pp.2030-2052
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• 2023

Analysis of a bipartite (two-mode) network is a significant research area to understand the formation of social communities, economic systems, drug side effect topology, etc. in complex information systems. Most of the previous works talk about a projection-based model or latent feature model, which predicts the link based on singular similarity. The projection-based models suffer from the loss of structural information in the projected network and the latent feature is hardly present. This work proposes a novel method for link prediction in the bipartite network based on an ensemble of composite similarities, overcoming the issues of model-based and latent feature models. The proposed method analyzes the structure, neighborhood nodes as well as latent attributes between the nodes to predict the link in the network. To illustrate the proposed method, experiments are performed with five real-world data sets and compared with various state-of-art link prediction methods and it is inferred that this method outperforms with ~3% to ~9% higher using area under the precision-recall curve (AUC-PR) measure. This work holds great significance in the study of biological networks, e-commerce networks, complex web-based systems, networks of drug binding, enzyme protein, and other related networks in understanding the formation of such complex networks. Further, this study helps in link prediction and its usability for different purposes ranging from building intelligent systems to providing services in big data and web-based systems.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2022년도 추계학술대회
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• pp.103-103
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• 2022

Ganghwaljetongyeum (GHJTY) is a complex herbal decoction comprising 18 plants; it is used to treat arthritis. In order to develop a new anti-arthritic herbal medication, we selected 5 out of 18 GHJTY plants by using bioinformatics analysis. The new medication, called ChondroT, comprised water extracts of Osterici Radix, Lonicerae Folium, Angelicae Gigantis Radix, Clematidis Radix, and Phellodendri Cortex. This study was designed to investigate its chondroprotective and anti-inflammatory effects to develop an anti-arthritic herb medicine. ChondroT was validated using a convenient and accurate high-performance liquid chromatography. photodiode array (HPLC-PDA) detection method for simultaneous determination of its seven reference components. The concentrations of the seven marker constituents were in the range of 0.81-5.46 mg/g. The chondroprotective effects were evaluated based on SW1353 chondrocytes and matrix metalloproteinase 1 (MMP1) expression. In addition, the anti-inflammatory effects of ChondroT were studied by Western blotting of pro-inflammatory enzymes and by enzyme-linked immunosorbent assay (ELISA) of inflammatory mediators in lipopolysaccharides (LPS)-induced RAW264.7 cells. ChondroT enhanced the growth of SW1353 chondrocytes and also significantly inhibited IL-1β-induced MMP-1 expression. However, ChondroT did not show any effects on the growth of HeLa and RAW264.7 cells. The expression of cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) was induced by LPS in RAW264.7 cells, which was significantly decreased by pre-treatment with ChondroT. In addition, ChondroT reduced the activation of NF-κB and production of inflammatory mediators, such as IL-1β, IL-6, PGE2, and nitric oxide (NO) in LPS-induced RAW264.7 cells. These results show that ChondroT exerted a chondroprotective effect and demonstrated multi-target mechanisms related to inflammation and arthritis. In addition, the suppressive effect was greater than that exhibited by GHJTY, suggesting that ChondroT, a new complex herbal medication, has therapeutic potential for the treatment of arthritis.

• Journal of Microbiology and Biotechnology
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• 제16권8호
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• pp.1269-1275
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• 2006

The selection of multienzyme complex-producing bacteria under aerobic condition was conducted for improving the degradation of lignocellulosic substances. The criteria for selection were cellulase and xylanase enzyme production, the presence of cellulose-binding domains and/or xylan-binding domains in enzymes to bind to insoluble substances, the adhesion of bacterial cells to insoluble substances, and the production of multiple cellulases and xylanases in a form of a high molecular weight complex. Among the six Bacillus strains, isolated from various sources and deposited in our laboratory, Paenibacillus curdlanolyticus B-6 strain was the best producer of cellulase and xylanase enzymes, which have both cellulose-binding factors (CBFs) and xylan-binding factors (XBFs). Moreover, multiple carboxymethyl cellulases (CMCases) and xylanases were produced by the strain B-6. The zymograms analysis showed at least 9 types of xylanases and 6 types of CMCases associated in a protein band of xylanase and cellulase with high molecular weight. These cells also enabled to adhere to both avicel and insoluble xylan, which were analyzed by scanning electron microscopy. The results indicated that the strain B-6 produced the multienzyme complex, which may be cellulosome or xylanosome. Thus, P. curdlanolyticus B-6 was selected to study the role and interaction between the enzymes and their substrates and the cooperation of multiple enzymes to enhance the hydrolysis due to the complex structure for efficient cellulases and xylanases degradation of insoluble polysaccharides.

• 한국수산과학회지
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• 제31권6호
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• pp.875-881
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• 1998

젓갈 및 자건품으로 소비량이 많은 멸치의 기능특성해석 및 기능성 조미 소재 제조의 일환으로 단백질 분해효소에 의한 멸치 육단백질 가수분해물의 peptide-nitrogen 생성량과 ACE 저해작용을 검토하였다. 소화효소와 식품공업용 단백질분해효소를 이용한 탈지 멸치육 가수분해물의 $50\%$ ethanol 가용성 peptide-nitrogen 생성량은 반응 8시간을 전후로 하여 거의 일정수준에 도달하였고, ACE 저해효과 역시 높게 나타났다. 따라서, 가수분해 8시간째의 각 효소 가수분해물의 peptide-nitrogen의 함량과 ACE 저해효과를 검토한 결과, 소화효소의 경우, $\alpha$-chymotrypsin으로 가수분해시켰을 때, $50\%$ ethanol 가용성 peptide-nitrogen의 생성량과 ACE 저해효과가 높은 것으로 나타났다 또한, 식품공업용 단백질분해 효소를 사용한 경우는 Alcalase 0.6L를 사용하였을 때가 $50\%$ ethanol 가용성 peptide-nitrogen의 생성량 및 ACE 저해효과가 가장 우수하였고, Protamex에 의해서는 $50\%$ ethanol 가용성 peptide-nitrogen의 생성량은 적었지만, ACE 저해효과는 높게 나타났다. ACE 저해효과가 우수한 멸치육 효소 가수분해물의 $50\%$ ethanol 가용성 획분의 아미노산 조성은 대부분의 가수분해물에서 glutamic acid의 함량이 가장 많았고, 그 다음으로 aspartic acid. cysteine 및 leucine의 순이었다.

• 생태와환경
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• 제36권2호통권103호
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• pp.108-116
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• 2003

부영양화 현상을 나타내는 석촌호수와 팔당호의 표층수와 저니로부터 178개의 균주를 분리한 후, Anabaena cylindrica lawn 상에서 plaque를 형성하는 9개의 균주를 선별하였으며 이들 중에서 남조류 생장 억제 능력이 가장 우수한 AK-07를 선발하였다. AK-07의 특성과 16S rDNA의 염기 서열 분석을 기초로 하여 유연관계를 조사한 결과, 형태적, 생리적 생화학적 특징들은 Acinetobacter속의 특성들과 유사하였으며, 165 rDNA의 염기 서열 분석한 결과는 Acinetobacter johnsonii와 99.5%의 유사성을 나타내어, Acinetobacter johnsonii AK-07로 명명하였다. 남조류 분해 특성을 조사하기 위해서, AK-07를 A. cylindrica와 혼합 배양시 접종 2일 후에 남조류의 분해가 관찰되었고, 접종 10일 후에는 남조류가 완전히 사멸하였으며, AK-07의 세포 수는 $8\;{\times}\;10^8\;cfu\;ml^{-1}$까지 증가하였다. 그러나 배양 상등액을 A. cylindrica와 혼합 배양 하였을 때에는 남조류의 분해는 관찰 되지 않았다. 따라서 AK-07는 남조류를 직접 접촉하여 분해하는 것으로 사료되어, AK-07에 세포에 존재하는 효소의 활성을 조사한 결과 Pretense와 glycanases중에서 ${\beta}$-Xylosidase의 활성이 가장 높았으며, Alginase, Laminarinase, Lipase, ${\beta}$-Galactosidase 및 ${\beta}$-Glucosidase의 활성도 높은 수준으로 관찰되었다. A. johnsonii AK-07은 A. cylindrica의 polysaccharides나 peptidoglycans를 monosaccharides이나 저분자 유기물로 분해하는 것으로 여겨진다.

• 한국식품저장유통학회지
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• 제30권2호
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• pp.287-299
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• 2023

효소 및 미생물 복합제를 사용하여 인비트로 발효 루왁커피를 제조하여 non-fermented coffee beans(NFC)과 fermented coffee beans(FC)의 커피 품질을 비교하였다. 총유리아미노산 함량은 NFC가 254.01±4.89 mg/mL, FC가 264.15±16.80 mg/mL로 FC의 함량이 다소 높은 것으로 확인되었다. 이때 NFC는 glutamic acid, γ-aminon-butyric acid 등이 높았으나, FC는 lysine, leucine, valine 등 필수아미노산의 함량이 높았다. 커피 생두의 발효과정은 sucrose의 감소와 fructose 및 glucose의 유의적인 증가를 가져왔다. 커피 추출물의 색도는 NFC에 비해 FC 시료에서 높은 명도(L)와 적색도(a) 및 황색도(b)를 보였다. 카페인 함량은 NFC 1,130.22±1.55 ㎍/mL, FC 696.94±0.04 ㎍/mL로써 발효 후 약 38%의 카페인이 감소되었다. 폴리페놀 및 클로로겐산 함량은 NFC에서 각각 2.31±0.01 mg GAE/mL와 531.81±27.32 ㎍/mL, FC에서 각각 2.03±0.07 mg GAE/mL와 264.46±2.47 ㎍/mL로 발효에 따라 떫은맛 관련 성분의 함량이 유의적으로 감소됨을 알 수 있었다. 전자코 분석에서 NFC와 FC의 휘발성 향성분의 차이가 뚜렷함이 확인되었고, methylethyl formate, 2-methyl-1, 3-cyclopentadiene, 2-chloro-2-methylbutane, 2-methylbutanal 등의 휘발성 화합물이 발효 후 높은 강도로 감지되었다. 관능 평가에서는 NFC 추출물보다 FC 추출물의 aroma, body, aftertaste, overall에서 높은 관능 평점을 보여주었다(p<0.001). 이상의 결과에서 효소 및 미생물 복합제를 사용한 커피 생두의 발효는 유효 성분들의 변화를 일으켜 커피 원두의 로스팅 과정 중 Maillard 반응을 촉진함으로써, 향미가 증가되고 카페인 함량이 감소된 인비트로 루왁 커피의 제조 가능성을 시사하였다.

• 한국식품영양학회지
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• 제9권3호
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• pp.294-298
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• 1996

By the 505 chromotest which utilized Escherichia bolt PQ 37, Korean medicinal plants had been screened to Investigate the antimutagenic effect to aflatoxin B1(AFBl). Ikmocho(IMC, Leonurus sibiricus L.) was extracted with hot water. The extract was not found to be mutagenic in the Salmonella mutation test with or without metabolic activation, and the extract was showed to possess the antimutagenic properties towards AFB1-induced metation. The mutagenicity of AFB1 was inhibited by methanol soluble fracstion (IMC-MS) in dose-dependent. However, water-soluble fraction exhibited comutagenic activity. The greatest inhibitory effect of IMC-MS on AFB1 mutagenicity occurred when IMC-MS was first incubated, AFB1 followed by a second incubation with the cells and 59 mixture. Also lower inhibition was occurred when S9 mixtures were first incubated, with IMC-MS followed by a second incubation with AFBI. The results of the sequential incubation study support the probability that one mechanism of inhibition could involve the formation of chemical complex between IMC-MS and AFB1 rather than deactivation of S9 enzyme.

• BMB Reports
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• 제39권2호
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• pp.223-227
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• 2006

Dihydrolipoamide dehydrogenase (E3) belongs to the pyridine nucleotide-disulfide oxidoreductase family including glutathione reductase and thioredoxin reductase. It catalyzes the reoxidation of dihydrolipoyl moiety of the acyltransferase components of three $\alpha$-keto acid dehydrogenase complexes and of the hydrogen-carrier protein of the glycine cleavage system. Isoleucine-51 of human E3, located near the active disulfide center Cys residues, is highly conserved in most E3s from several sources. To examine the importance of this highly conserved Ile-51 in human E3 function, it was substituted with Ala using site-directed mutagenesis. The mutant was expressed in Escherichia coli and highly purified using an affinity column. Its E3 activity was decreased about 100-fold, indicating that the conservation of the Ile-51 residue in human E3 was very important to the efficient catalytic function of the enzyme. Its altered spectroscopic properties implied that conformational changes could occur in the mutant.

• Journal of Microbiology and Biotechnology
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• 제19권12호
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• pp.1527-1535
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• 2009

Polyphosphate (polyP) plays diverse physiological functions in prokaryotes and eukaryotes, but most of their detailed mechanisms are still obscure. Here, we show that deletion of polyphosphate kinase (PPK), the principal enzyme responsible for synthesis of polyP, resulted in augmented expression of cAMP receptor protein (CRP) and rpoS and lowered $H_2O_2$ sensitivity in Salmonella Typhimurium ATCC14028. The binding of cAMP-CRP complex to rpoS promoter and further stimulation of its transcription were proved through electrophoretic mobility shift assay, lacZ fusion, and exogenous cAMP addition, respectively. The rpoS expression increased in cpdA (cAMP phosphodiesterase coding gene) mutant, further suggesting that cAMP-CRP upregulated rpoS expression. These results demonstrate that PPK affects oxidative stress response by modulating crp and rpoS expression in S. Typhimurium.